Ag3.6#

The Ag3.6: Anopheles gambiae data resource contains single nucleotide polymorphism (SNP) calls, copy number variant (CNV) calls and SNP haplotypes from whole-genome sequencing of 1404 mosquitoes.

More information about this release can be found in the data resource website.

This page provides an introduction to open data resources released as part of Ag3.6.

If you have any questions about this guide or how to use the data, please start a new discussion on the malariagen/vector-open-data repo on GitHub. If you find any bugs, please raise an issue.

Terms of use#

Please note that, unless otherwise stated, all data on this release are subject to a publication embargo, described further in the Anopheles gambiae genomic surveillance project terms of use.

The publication embargo for all data on this release will expire on the 17th of November 2025.

If you have any questions about the terms of use, please email data@malariagen.net

Partner studies#

  • 1273-VO-ZM-MULEBA - PAMCA Anopheles genomics programme - Seasonality and impact of vector control interventions on population genetics of Anopheles funestus and Anopheles gambiae malaria vectors in Zambia

  • 1279-VO-CI-KOFFI - PAMCA Anopheles genomics programme - Strengthening malaria vector surveillance in Cote d’Ivoire: An investigation into genetic diversity and gene flow data gap in insecticide resistant Anopheles gambiae

  • 1280-VO-ZA-MUNHENGA - PAMCA Anopheles genomics programme - Genetic structuring in the major malaria vector Anopheles arabiensis and implication on vector control in South Africa

  • 1288-VO-UG-DONNELLY - LLIN Evaluation in Uganda Project (LLINEUP)

Whole-genome sequencing and variant calling#

All samples in Ag3.6 have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis.

For further information about the sequencing and variant calling methods used, please see the methods page.

Data hosting#

Data from Ag3.6 are hosted by several different services.

The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as MyBinder and Google Colab. Further information about analysing these data in the cloud is provided in the cloud data access guide.

Sample sets#

The samples included in Ag3.6 have been organised into 5 sample sets.

Each sample set corresponds to a set of mosquito specimens from a contributing study. Study details can be found in the partner studies webpages listed above.

sample_set sample_count
study_id
1273-VO-ZM-MULEBA 1273-VO-ZM-MULEBA-VMF00176 201
1279-VO-CI-KOFFI 1279-VO-CI-KOFFI-VMF00173 379
1280-VO-ZA-MUNHENGA 1280-VO-ZA-MUNHENGA-VMF00165 178
1280-VO-ZA-MUNHENGA 1280-VO-ZA-MUNHENGA-VMF00178 163
1288-VO-UG-DONNELLY 1288-VO-UG-DONNELLY-VMF00168 483

Here is a more detailed breakdown of the samples contained within this sample set, summarised by country, year of collection, and species:

taxon arabiensis coluzzii gambiae unassigned
study_id sample_set country year
1273-VO-ZM-MULEBA 1273-VO-ZM-MULEBA-VMF00176 Zambia 2018 0 0 12 0
2020 0 0 113 0
2021 0 0 76 0
1279-VO-CI-KOFFI 1279-VO-CI-KOFFI-VMF00173 Cote d'Ivoire 2020 0 287 92 0
1280-VO-ZA-MUNHENGA 1280-VO-ZA-MUNHENGA-VMF00165 South Africa 2020 20 0 0 0
2021 158 0 0 0
1280-VO-ZA-MUNHENGA-VMF00178 South Africa 2020 94 0 0 0
2021 69 0 0 0
1288-VO-UG-DONNELLY 1288-VO-UG-DONNELLY-VMF00168 Uganda 2017 0 0 182 0
2018 0 0 166 1
2019 0 0 134 0

Note that there can be multiple sampling sites represented within the same sample set.

Further reading#

We hope this page has provided a useful introduction to the Ag3.6 data resource. If you would like to start working with these data, please visit the cloud data access guide or the data download guide or continue browsing the other documentation on this site.

If you have any questions about the data and how to use them, please do get in touch by starting a new discussion on the malariagen/vector-data repository on GitHub.